It appears that controlled-$U$ type operation is the bedrock to many quantum algorithms, for instance, phase estimation and amplitude estimation. These algorithms systematically employs the controlled-$U$ type operation on the a state, say $|\psi\rangle$, stored in an oracle register while retaining one qubit in the computational register as the control bit. Consider a general case: The control bit is brought into a superposition $\frac{1}{\sqrt{2}}(|0\rangle + |1\rangle)$ and the $|\psi\rangle$ is not an eigenstate of operator $U$, meaning $U|\psi\rangle = |\phi\rangle$. Now, we execute the controlled-$U$ operation to have
$\frac{1}{\sqrt{2}}(|0\rangle + |1\rangle)\otimes|\psi\rangle \xrightarrow{c-U}\frac{1}{\sqrt{2}}(|0\rangle\otimes|\psi\rangle + |1\rangle \otimes|\phi\rangle)$
where this basically implies that the control bit is entangled with the state in the oracle register. (Phase estimation is a special case where operator $U$ 'squeezes' out a phase factor $U|\psi\rangle = e^{\theta}|\psi\rangle$ and once this phase factor is considered back-kicked to state $|1\rangle$, the states in computational and oracle registers are separable.)
Here is what puzzles me. First, when we retain another bit in computational register as the control bit and apply $U$ on the oracle register, to what state are we actually applying this operator $U$? It appears in the most general case the resulting state of the control bit and the oracle register needs to be viewed as one state. Second, how does the matrix that represents this controlled-$U$ operator look like? To be more concrete, take the following 3-bit computational register as example,
$\frac{1}{\sqrt{2}}(|0\rangle + |1\rangle)\otimes\frac{1}{\sqrt{2}}(|0\rangle + |1\rangle)\otimes\frac{1}{\sqrt{2}}(|0\rangle + |1\rangle)$
retaining the second bit as control and apply $U$ (on the oracle register), how does that matrix look like?